Description

Converts MAF alignments in another format.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

maf{:bash}

:file

Multiple Alignment Format (MAF) file, optionally compressed with gzip

*.{maf.gz,maf}

format{:bash}

:string

Output format (one of axt, bam, blast, blasttab, cram, chain, gff, html, psl, sam, or tab)

meta2{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

fasta{:bash}

:file

Genome file in FASTA format for CRAM conversion. If compressed it must be done in BGZF format (like with the bgzip tool).

*.{fasta,fasta.gz,fasta.bgz,fasta.bgzf}

meta3{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

fai{:bash}

:file

Genome index file needed for CRAM conversion.

*.fai

meta4{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

gzi{:bash}

:file

Genome index file needed for CRAM conversion when the genome file was compressed with the BGZF algorithm.

*.gzi

meta5{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

dict{:bash}

:file

Samtools dictionary of the genome file.

*.dict

Output

name:type
description
pattern

alignment{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.{axt.gz,bam,bed.gz,blast.gz,blasttab.gz,chain.gz,cram,gff.gz,html.gz,psl.gz,sam.gz,tab.gz}{:bash}

:file

Pairwise alignment exported to Axt, BAM, BED, BLAST, Chain, CRAM, GFF, HTML PSL, SAM or Tab format.

*.{axt.gz,bam,bed.gz,blast.gz,blasttab.gz,chain.gz,cram,gff.gz,html.gz,psl.gz,sam.gz,tab.gz}

versions_last{:bash}

${task.process}{:bash}

:string

The name of the process

last{:bash}

:string

The name of the tool

lastal --version | sed 's/lastal //'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

last{:bash}

:string

The name of the tool

lastal --version | sed 's/lastal //'{:bash}

:eval

The expression to obtain the version of the tool

Tools

last
GPL v3-or-later

LAST finds & aligns related regions of sequences.

gitlab.com/mcfrith/last gitlab.com/mcfrith/last/-/blob/main/doc https://gitlab.com/mcfrith/last
included in
pairgenomealign
maintainer
Github user charles-plessy
get in touch
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